Dear Members,

Is there any way to pre-filter the dataset in LIMMA before going on to
differential expression analysis?

I am using Agilent microarrays and would really like to filter out
genes/spots based on flags. Is this possible in LIMMA? Or is there any
better way to filter than using flags in LIMMA?

My dataset has a lot of genes and I really think I should use stringent
filtering before going onto analysis part. I am thinking of using kind of
code given in
http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma
(Thanks
to John Mattick <http://matticklab.com/index.php?title=John_Mattick> and Gordon
Smyth).

I would also be extremely grateful if someone could share a bit of such
codes since I am just a newbie.

Thanks a lot in advance for your help.

Kart

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